Surface

Surface

Purpose

This program allows you to generate surfaces for a mathematical phantom and combine these two surfaces or any other two surfaces in a volume mask for 3D reconstructions.

With respect to the surface generation the process intends to produce the surface which would be generated by a surface technique like AFM or metal shadowing. So for each(X,Y) it returns theZ coordinate of the voxel which is nearest to the phantom but it is not touching it. The top surface is defined when the height probe goes fromZ- toZ+ (remember that in Xmipp theZ axis is pointing to the floor) and the bottom surface when the probe goes fromZ+ toZ-. If there is no phantom along the(X,Y) position then that height is set to the first point which is outside the phantom in that direction.ztop andzbottom control until which height we can insert the probe, the probe cannot go further this point, if the phantom is not reached still then we have to say that we don't know the height for that point but as minimum isztop orzbottom. If the ray reaches the end of the volume and the phantom is not found then the corresponding surface value is the coordinate of the first voxel checked outside the volume.

As for the surface combination, the surface must meet the convention used for generating them, then the output is a mask volume which represents the knowledge we have about the protein. Where the mask is 0 it means that we know that there is no protein at all there, and where the mask is 1 we are saying that we don't know a word about the volume there

Usage

$ surface ...

Parameters

• `` Input file with the phantom description
• `` Output volume with the required surfaces as masks for a reconstruction process
• `` Computes the bottom surface (fromZ+ to`Z-`) and stores it in the given filename. Use`-zbottom` to limit the maximum plane reached by the height probe
• `` This is the maximumZ that the height probe is allowed to reach when computing the bottom surface
• `` Computes the top surface (fromZ- to`Z+`) and stores it in the given filename. Use`-ztop` to limit the maximum plane reached by the height probe
• `` This is the maximumZ that the height probe is allowed to reach when computing the top surface
• `` This isZ dimension for the output volume when two real surfaces are provided instead of being generated internally by this program. This parameter can also be used to generate fix the size of the output mask

Examples and notes

Surfaces and volume masks from phantoms

The following is an example of a 2D phantom to illustrate the ideas of how surface work. The extension to 3D is straightforward.

/phantom2D.gif

Without maximum height restrictions the top and bottom surfaces of it are obtained by

$ surface -i phantom2D -top top_surface
$ surface -i phantom2D -bottom bottom_surface

and the corresponding values are

top_surface:

5

-1

-2

-3

-3

-2

5

5

5

and the`bottom_surface` is:

-5

1

2

2

2

1

-5

-5

-5

You can generate the volume mask as well using either the top surface, the bottom one or both. To do so to the previous commands you have to add the argument`-o [output mask]` (you may add`-zdim` to change the size of the output volume). The result for a big sphere not allowing the probe to go further by two planes is

/mask.gif

Combination of Real Surfaces

So far we have been working with surfaces which were coming from a phantom, but what if we want to combine two real surfaces? This is the right structure for doing so

$ surface -top top_surface -bottom bottom_surface -o mask

One of the two surfaces may be left out if don't have it.

--Main.AlfredoSolano - 30 Jan 2007